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Sage-Bionetworks
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Genie
Validation and processing of GENIE files
https://genie.synapse.org/
MIT License
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Update configure maf docstring
#578
rxu17
closed
1 week ago
1
Update doctsrings of maf functions
#577
rxu17
closed
1 month ago
1
[GEN-1429] Add variant_classification as known string col
#576
rxu17
closed
2 months ago
1
Update docstring for cna's validateSymbol function
#575
rxu17
closed
2 months ago
1
[GEN-703] Validation status with version
#574
thomasyu888
closed
1 month ago
3
[GEN-1408] PoC: Remove rows of data containing SEQ_ASSAY_ID that are filtered out
#573
thomasyu888
opened
3 months ago
1
[GEN-1348] Allow in mapping tables
#572
rxu17
closed
3 months ago
1
[GEN-1299] align col names
#571
thomasyu888
closed
1 month ago
2
[GEN-1326] Remove panel overlap charts
#570
thomasyu888
closed
1 month ago
2
[GEN-1325] Remove section on flagged mutations
#569
thomasyu888
closed
1 month ago
3
[GEN-1330] Setup staging pipeline
#568
rxu17
closed
1 month ago
4
[GEN-1313] Export detailed columns for NAACCR codes
#567
danlu1
closed
4 months ago
2
[GEN-1109] Setup base mkdocs for genie
#566
rxu17
closed
4 months ago
4
[GEN-1294] pin r-base version and upgrade to Node 20
#565
danlu1
closed
5 months ago
2
[GEN-1285] Remove row based validation
#564
danlu1
closed
5 months ago
1
[GEN-1285] Remove row-based validation error message
#563
danlu1
closed
5 months ago
1
[GEN-1263] Fix bed file duplicates
#562
rxu17
closed
4 months ago
5
[GEN-867] Add validation rule to check if INT_DOD >= INT_CONTACT
#561
danlu1
closed
5 months ago
1
[GEN-868] add year death validation
#560
danlu1
closed
5 months ago
2
[GEN-178] Update to pandas 2.0 and upgraded synapseclient
#559
rxu17
opened
5 months ago
2
[GEN-1000] Refactor and sort unmapped oncotree codes in validation message
#558
rxu17
closed
5 months ago
2
[GEN-1237] Add documentation to maf allele validation
#557
rxu17
closed
6 months ago
1
[GEN-1164] add workflow to build docker image and push it to ghcr
#556
danlu1
closed
6 months ago
1
[GEN-997] update method to concatenate columns for dataframe
#555
danlu1
closed
5 months ago
2
[GEN-996] convert the clinical template columns from a set to a list
#554
danlu1
closed
5 months ago
2
[GEN-1067] add functionality to warn for identical ref and tsa2
#553
danlu1
closed
6 months ago
2
[GEN-1191] Add file logging
#552
rxu17
closed
7 months ago
1
[GEN-1163] Hotfix for annotation-tools
#551
rxu17
closed
7 months ago
1
[GEN-1065] Use OIDC with pypi in genie package publishing
#550
rxu17
closed
7 months ago
2
[GEN-974] Allow NaN, nan and NA strings for mutation data
#549
rxu17
closed
8 months ago
1
[GEN-1076] Exclude genomic_location_explanation from release
#548
rxu17
closed
8 months ago
4
[GEN-1078] HOTFIX: Add in new known string columns as MSK added new columns into maf file
#547
thomasyu888
closed
8 months ago
1
[GEN-1028] Generate failed annotations report dashboard
#546
rxu17
closed
8 months ago
6
[GEN-1027] Store failed annotations error report
#545
rxu17
closed
8 months ago
3
[GEN-1026] Output annotation error report
#544
rxu17
closed
9 months ago
1
[GEN-1018] Update __main__.py and validate.py
#543
Chelsea-Na
closed
9 months ago
1
Update docs
#542
rxu17
closed
10 months ago
0
[GEN-977] update annotation-tools version
#541
rxu17
closed
10 months ago
0
[GEN-973] Fix bed file-clinical file cross-validation
#540
rxu17
closed
10 months ago
0
[GEN-809] Validate allele columns
#539
rxu17
closed
11 months ago
0
[GEN-905] - Change error of start position > end position to a warning
#538
thomasyu888
closed
12 months ago
0
[GEN-834] Disable data guide generation
#537
rxu17
closed
1 year ago
0
[GEN-846] & [GEN-845] Ignore case and allow underscores in cross-validate
#536
rxu17
closed
1 year ago
0
[GEN-851] Hotfix pin cbioportal repo version
#535
rxu17
closed
1 year ago
0
[GEN-833] Remove support for python 3.7, pin synapseclient
#534
rxu17
closed
1 year ago
0
[GEN-738] Add variant position validation for maf file
#533
rxu17
closed
1 year ago
0
[GEN-498] Remove fusion files from public release
#532
rxu17
closed
1 year ago
0
[GEN-498] Remove fusion files from public release
#531
rxu17
closed
1 year ago
0
[GEN-756] Fix maf validation
#530
rxu17
closed
1 year ago
0
[GEN-478] Fix BIRTH_YEAR redaction
#529
thomasyu888
opened
1 year ago
1
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